More than 100,000 veterans have been identified as experiencing long wait times for medical appointments with nearly a quarter of those waiting 90 to 120 days for care, according to an audit released Monday by the Veterans Affairs Department.

The review of 731 VA medical centers and clinics found that VA’s complicated appointment system and pressures placed on schedulers to meet a 14-day target for getting patients into care — a goal auditors deemed unrealistic — created confusion and represent an “organizational leadership failure” at VA.

The audit found that 13 percent of scheduling staff said supervisors had told them to alter appointment dates to make wait times appear shorter, while 8 percent said they used other systems to track patients’ appointments besides VA’s approved electronic system or health records system.

The audit found 112 facilities in need of further review, meaning that information uncovered at the facilities triggered a more thorough investigation. The facilities include some medical centers where whistleblowers have stepped forward with allegations of scheduling fraud, including San Antonio; Cheyenne VA Medical Center, Wyoming; and Atlanta VA Medical Center.

The Phoenix VA Health System — “ground zero” for the scandal of delayed patient care at VA — is not on the list. But the VA inspector general is conducting a thorough investigation into the issues at Phoenix and has taken steps to expedite care to veterans there.

According to a senior VA official, the department has contacted 50,000 of those found waiting for care by auditors.

The problems at the facilities, according to auditors, include staff:

■Instructed to alter desired appointment dates;

■Keeping manual logs of appointments;

■Canceling appointments, and;

■Canceling consults.

According to the report, the biggest obstacle to patients getting a timely appointment was lack of available time slots, followed by problems with the 14-day wait list requirement.

A shortage of clerical staff also was noted as a problem.

Acting Veterans Affairs Secretary Sloan Gibson said Thursday that VA is working to “earn back the trust of veterans.”

He has removed a performance metric on senior VA manager performance reviews that required them to meet a 14-day standard for appointment times and served as an “incentive to falsify information.”

He also pledged to hold anyone found to be involved in malfeasance accountable and took away 2014 bonuses for VA senior executive service employees.

A senior VA official said Monday the department also has initiated a hiring freeze at its Washington, D.C., headquarters and all regional offices so that VA’s human resources offices can concentrate on hiring clinical staff and fill positions related to patient care.

“This action will begin to remove bureaucratic obstacles and establish responsive, forward leaning leadership,” according to a VA statement.

VA has contacted all 1,700 veterans who were not on the Phoenix center’s official appointment wait list system to expedite their care. According to Gibson, 18 vets on that off-the-books list were dead, some of whom VA had “tried to contact multiple times” and others who needed end-of-life care.

In Phoenix, the department dispatched mobile medical units to accelerate patient care and has authorized wider use of non-VA care for patients who cannot be seen in a timely manner.

A similar approach will be used at all VA facilities identified in the audit as “the most challenged,” the senior official said Monday during a conference call with reporters.

VA expects to spend at least $3 million in the next several months on the effort.

“We are facing a systemic issue. It involves the tracking of patient wait times and the integrity of our scheduling practices. We will learn from this access audit and it will make us a better system,” the senior official said.

The House Veterans’ Affairs Committee will hold a hearing Monday evening to continue its focus on the problems of the VA’s scheduling system.

The Senate this week also may reveal the details of a comprehensive veterans’ bill forged by Sens. Bernie Sanders, I-Vt., and John McCain, R-Ariz.

Among the issues identified by Sanders as a problem in VA is its antiquated scheduling system. The senior official said Monday the system software package was built in 1985.

“Think about it — that was before the Internet. ... It’s going to need an update,” the senior official said.